Means and Methods to Induce Apomixis in Plants

ABSTRACT

The present invention relates to nucleic acid molecules for use in inducing apomixis in a plant, transgenic cells, in particular transgenic plant cells, comprising said nucleic acid molecule, transgenic plants, in particular plant seeds, comprising said nucleic acid molecule, methods for inducing apomixis in a plant, methods for the production of apomictic plants and uses thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of application Ser. No. 16/150,957,filed Oct. 3, 2018, which is a Continuation of 371 U.S. National Phaseapplication Ser. No. 14/123,069, filed Nov. 27, 2013, issued as U.S.Pat. No. 10,131,919, which claims priority to PCT/EP2012/059808, filedMay 25, 2012 based on European Patent Application No. 11168075.7 filedon May 30, 2011, the contents of which applications, including theSequence Listing of 329810 bytes filed on Nov. 27, 2013 in U.S. NationalPhase application Ser. No. 14/123,069, are incorporated herein byreference in their entireties.

The present invention relates to nucleic acid molecules for use ininducing apomixis in a plant, transgenic cells, in particular transgenicplant cells, comprising said nucleic acid molecule, transgenic plants,in particular plant seeds, comprising said nucleic acid molecule,methods for inducing apomixis in a plant, methods for the production ofapomictic plants and uses thereof.

Naturally occurring vegetative, non-sexual reproduction in plantsthrough seeds, also called apomixis, is a genetically controlledreproductive mechanism of plants primarily found in some polyploidnon-cultivated species. Various types of apomixis, inter aliagametophytic and sporophytic, can be distinguished. In sporophyticapomixis also called adventitive embryony, a somatic embryo develops notfrom the gametophyte but directly from the cells of the nucellus, ovarywall or integuments. Somatic embryos from surrounding cells invade thesexual ovary, one of the somatic embryos out-competes the other somaticembryos and the sexual embryo, and utilizes the produced endosperm.

Gametophytic apomixis is a naturally-occurring type of asexual seedformation whereby progeny, which are clonal to the maternal genotype,are produced from meiotically-unreduced embryo sacs, i. e. the femalegametophyte. Most gametophytic apomictic species are found in theAsteraceae, Rosaceae and Poaceae, where they have arisen independentlyand recurrently. Polyploidy, facultative apomixis (both sexual andapomictic seed production within one individual), and faster developmentof the apomeiotic ovule relative to the sexual one are traits which areshared among most of these taxa. Apomixis is derived from sex, and threeindependent developmental steps must be acquired for a sexual plant toproduce seeds apomictically: the formation of an unreduced megaspore,that means the formation of an embryo sac having the same ploidy as thesomatic cells of the mother plant from a meiotically-unreduced megaspore(diplospory, apomeiosis) or from nucellar cell (apospory), thesubsequent development of an embryo from an unreduced egg in the absenceof fertilization (parthenogenesis) and fertilization of the binucleatecentral cell to form a functional endosperm (pseudogamy). The term“apomeiosis” covers both apospory and diplospory. Theapomeiotically-derived embryo thus receives its entire genome throughthe female line. As these components are under separate genetic control,it has been difficult to envision how all three could evolve in unisonin a sexual ancestor considering random mutations, since the expressionof any single step would decrease the fitness of its sexual carrier. Itis widely accepted that apomictic seed development results fromderegulation of the sexual development pathway, which would bemanifested at multiple loci simultaneously. In wild apomictic taxa, thiscoordinated deregulation is hypothesized to be influenced by globalregulatory changes resulting from hybridization and/or polyploidy(Grossniklaus, 2001, From sexuality to apomixis: Molecular and geneticapproaches, In: The flowering of apomixis: From Mechanisms to GeneticEngineering, 168-211).

Recent reports analyse the gene expression of apomeiosis, that meansunreduced gamete formation, in microdissected ovules of Boechera, andwere able to identify quite a large number of differentially expressedalleles between sexual and apomeiotic ovules in a particular stage ofthe development, namely the megaspore mother cell (MMC) stage. Furtherstudies focussed on heterochrony of gene expression patterns over aseries of developmental stages in sexual and apomeiotic ovules (Sharbelet al., 2009, The Plant Journal, 58, 870-882, Sharbel et al., 2010, ThePlant Cell, 22, 655-671). However, although the state of the artexpectedly show that apomictic and sexual ovules are characterised byspecific molecular signatures, it does not provide any clue on how toinduce apomixis in a desired plant in a reliable and foreseeable manner,in particular by means of conventional gene transfer techniques.

In fact, one of the main difficulties in identifying the moleculargenetic mechanisms controlling apomixis is that the genomes of virtuallyall apomicts are both polyploidy and hybrid in nature. Althoughconsiderable efforts, including in-depth functional molecular analyses,have been undertaken to analyse the molecular framework underlyingapomictic phenomena, so far it still remains a challenge to controlseparately for the influences of either effect, both of which can havediverse regulatory consequences.

Engineering apomixis to a controllable, more reproducible trait wouldprovide many advantages in plant improvement and cultivar development.Apomixis would provide for true-breeding, seed propagated hybrids.Harnessing apomixis would, thus, greatly facilitate and accelerate theability of plant breeders to fix and faithfully propagate geneticheterozygosity and associated hybrid vigour in crop plants. Moreover,apomixis could shorten and simplify conventional breeding processes sothat selfing and progeny testing to produce or stabilize a desirablegene combination could be eliminated.

The controlled use of apomixis would therefore certainly simplifycommercial hybrid seed production. In particular, the need for physicalisolation of commercial hybrid production fields would be eliminated,available land could be used to grow hybrid seed instead of dividingspace between pollinators and male sterile lines and finally the need tomaintain parental line seed stocks would be eliminated.

Apomixis would provide for the use as cultivars of genotypes with uniquegene combinations since apomictic genotypes breed true irrespective ofheterozygosity. Genes or groups of genes could thus be fixed in supergenotypes. Every superior apomictic genotype from a sexual-apomicticcross would have the potential to be a cultivar. Apomixis wouldtherefore allow plant breeders to develop cultivars with specific stabletraits for such characters as height, seed and forage quality andmaturity.

Thus, the application of apomixis in agriculture is considered animportant enabling technology that would greatly facilitate the fixationand faithful propagation of genetic heterozygosity and associated hybridvigor in crop plants (Spillane, 2004, Nat Biotech 22(6), 687-691).

All these potential benefits which rely on the production of seed viaapomixis are presently, however, unrealized, to a large extent becauseof the problem of engineering apomictic capacity into plants ofinterest.

US 2002/0069433 A1 discloses methods for increasing the probability ofvegetative reproduction of a new plant generation wherein a gene whichencodes a protein acting in the signal transduction cascade triggered bythe somatic embryogenesis receptor kinase is transgenically expressed.US 2008/0155712 A1 discloses processes for identifying in a plant, inparticular maize, sequences responsible for apomictic development, inparticular by genome mapping. WO 99/35258 A1 discloses nucleic acidmarkers for an apospory specific genomic region from the genusPennisetum. U.S. Pat. No. 7,541,514 B2 discloses methods for producingapomictic plants from sexual plants by selecting, collecting andbreeding specific plant lines.

None of said disclosures provide means, in particular polynucleotides,which can easily be used in gene transfer methods to obtain in acontrollable and inexpensive way apomixis in plants.

The technical problem underlying the present invention is therefore toprovide means and methods to overcome the above-identified problems, inparticular to provide means and methods to introduce apomixis into aplant for instance by means of recombinant gene technology, inparticular by means of recombinant DNA transfer technology, inparticular to provide means and methods to induce apomixis in plants, inparticular in a controllable, foreseeable, reliable, easy andcost-effective way.

The present invention solves its underlying problem by the provision ofthe teaching of the independent claims, in particular by the provisionof nucleic acid molecules, in particular isolated nucleic acidmolecules, useful for inducing apomixis in plants, plant cells and plantparts containing said sequence as well as methods to induce apomixis inplants, methods to produce apomictic plants and uses thereof. Inparticular, the present invention solves its underlying technicalproblem by the provision of an isolated nucleic acid molecule for use ininducing apomixis in a plant comprising a polynucleotide which isselected from the group consisting of a) the polynucleotide defined inany one of SEQ ID No. 22 to 62, or a fully complementary strand thereof,b) a polynucleotide encoding a polypeptide with the amino acid sequencedefined in any one of SEQ ID No. 1 to 21, or a fully complementarystrand thereof, and c) a polynucleotide variant having a degree ofsequence identity of more than 70% to the nucleic acid sequence definedin a) or b), or a fully complementary strand thereof, preferably whereinthe sequence identity is based on the entire sequence. Preferably, thesequence identity is determined by BLAST analysis, preferably in theNCBI database, in particular by GAP analysis using Gap Weight of 50 andLength Weight of 3.

The present invention relates in a particularly preferred embodiment toan isolated nucleic acid molecule which comprises a polynucleotidecoding for a protein capable of inducing apomixis in a plant, preferablyin a plant ovule, preferably exhibiting an exonuclease activity in aplant ovule, which is selected from the group consisting of a1) thepolynucleotide defined in any one of SEQ ID No. 22 to 62, in particular23, 25, 27, 28, 29, 30, 33, 35, 37, 38, 40, 41, 43, 44, 47, 50 or 53, ora fully complementary strand thereof, b1) a polynucleotide encoding apolypeptide with the amino acid sequence defined in any one of SEQ IDNo. 1 to 21, preferably SEQ ID No. 4 to 9, SEQ ID No. 13 to 15 or SEQ IDNo. 19 to 21, or a fully complementary strand thereof, and c1) apolynucleotide variant having a degree of sequence identity of more than30%, 40%, 50% or, preferably 70% to the nucleic acid sequence defined ina1) or b1), or a fully complementary strand thereof, preferably whereinthe sequence identity is based on the entire sequence. Preferably, thesequence identity is determined by BLAST analysis, preferably in theNCBI database, in particular by GAP analysis using Gap Weight of 50 andLength Weight of 3 or any other suitable analysis.

The nucleic acid molecules of the present invention represent theso-called apollo gene, which means “Apomixis linked locus”, or areessential and specific parts thereof. Said gene, in particular itscoding sequence, codes for the apollo protein which upon expression inthe plant ovule leads to the production of apomictic seed.

The present invention also relates in a preferred embodiment to theabove-identified protein-coding polynucleotide which is in particularcharacterised by the presence of at least one specific duplicated markersequence in an exon, namely the fifth exon, of said sequence and whichrepresents a nucleotide stretch duplication. Preferably, said duplicatedmarker nucleotide sequence is given in SEQ ID No. 64 and itscorresponding amino acid sequence in SEQ ID No. 63.

Accordingly, the present invention also relates to an isolated nucleicacid molecule, which comprises a polynucleotide coding for a proteincapable of inducing apomixis in a plant, preferably in a plant ovule,preferably exhibiting an exonuclease activity in a plant ovule, whereinthe polynucleotide comprises a nucleic acid sequence selected from thegroup consisting of a2) the polynucleotide defined in any one of SEQ IDNo. 22, 23, 27, 28, 32 or 33, preferably 23, 28 or 33, or a fullycomplementary strand thereof, b2) a polynucleotide encoding apolypeptide with the amino acid sequence defined in any one of SEQ IDNo. 4, 5 or 6 or a fully complementary strand thereof, and c2) apolynucleotide variant having a degree of sequence identity of more than30%, 40%, 50% or, preferably 70% to the nucleic acid sequence defined ina2) or b2), or a fully complementary strand thereof, preferably whereinthe sequence identity is based on the entire sequence. Preferably, thesequence identity is determined by BLAST analysis, preferably in theNCBI database, in particular by GAP analysis using Gap Weight of 50 andLength Weight of 3 or any other suitable analysis.

The present invention advantageously provides polynucleotides, inparticular polynucleotides coding for a protein capable of inducingapomixis in a plant, namely the apollo protein, and polynucleotidescapable of functioning as regulatory elements for said coding sequence,in isolated and purified form. Furthermore, the present inventionprovides the teaching that plants, in particular their genome, compriseendogenously nucleotide sequences, hereinafter also called“polynucleotide” or “polynucleotide sequence”, coding said apolloprotein capable of inducing apomixis and its regulatory elements,hereinafter also called “endogenously present polynucleotide coding aprotein capable of inducing apomixis in a plant”. Thus, both the codingand the regulatory sequences as specified for instance in SEQ ID No. 37,40, 43, 46, 49 or 52 are usually endogenously present in various allelicstates in their natural and original genome environment in a plant,particularly in Brassicaceae, preferably Boechera, and are responsiblefor the development of a sexual or apomictic phenotype in the plant.According to the findings of the present invention in the naturallyoccurring sexually propagating plant, said nucleotide sequences in theirsexual allelic state, such as in SEQ ID No. 46, 49 or 52, however, arein the ovule of said plant repressed, that means not expressed, therebypreventing apomixis. In contrast, said polynucleotide in its apomicticallelic state, such as in SEQ ID No. 37, 40 or 43 is induced, that meansis expressed in the ovule of a plant propagating asexually, that meansan apomictic plant.

In particular, the invention is based on the teaching that in a plantovule of a sexually propagating plant the endogenously present genecoding for the apollo protein with an apomixis-inducing capacity issuppressed or inactivated in said tissue and therefore needs to beactivated in order to produce an apomictic plant. Both in sexually andapomictic plants the coding regions of the apollo gene in its apomicticand sexual allelic form, are functionally equivalent. Differences intheir expression are due to their different regulatory elementspreferably as specified in SEQ ID No. 57 to 62 and 65. In particular,apomictic regulatory elements, preferably those as identified in SEQ IDNo. 55, 57, 58 and 59, are in particular characterised by the presenceof a 20 base pair promoter insertion, in particular that of SEQ ID No.65, which leads to an ovule expression, i.e. expression in the ovule, ofa coding element linked to said regulatory element. The sexualregulatory element of the present invention is in particularcharacterised by the absence of such a promoter insert of SEQ ID No. 65and is represented in particular by a regulatory element as given in SEQID No. 56, 60, 61 or 62 and provides a somatic gene expression, but notan expression in the ovule, possibly due to being suppressed in saidtissue.

In particular, the invention therefore provides the teaching to modify,in particular activate or induce, that means to get said sequencesexpressed in order to achieve a plant of a desired phenotype, inparticular an apomictic phenotype. This can preferably be achieved byeither transforming a plant with expressible coding sequences for theapollo protein of the present invention for its expression in the plant,in particular a plant ovule, so as to provide the apomictic phenotype tosaid plant and its progeny or by transforming a plant with regulatorysequences of the present invention inducing the expression of theendogenously present polynucleotide coding for the present proteincapable of inducing apomixis, that means the apollo protein in saidplant. Furthermore, the present invention achieves its aim of providingan apomictic plant by transforming a plant with any nucleotide sequence,in particular any DNA molecule, which structurally interferes with therepressed regulatory element of an endogenously present apollo gene, inparticular polynucleotide sequence, capable of expressing a proteincapable of inducing apomixis in the plant, thereby derepressing saidapollo gene and allowing its expression in a plant ovule so as toproduce an apomictic plant.

Thus, the present invention foresees to introduce an exogenouspolynucleotide, in particular transgenic, coding sequence for the apolloprotein into a plant, so as to express said coding sequence in the plantovule. The invention also foresees in an alternative embodiment toactivate, that means to induce the expression of an endogenously presentapollo gene, in particular polynucleotide coding for the apollo proteincapable of inducing apomixis, that means to induce the endogenouslypresent apollo gene in the plant.

In the context of the present invention, the term “inducing theexpression of a gene—or polynucleotide—coding for protein capable ofinducing apomixis” therefore refers to the activation, hereinafter alsotermed derepression, of a regulatory element governing the expression ofsaid coding sequence, that means refers to the activation of expressionallowing the production of a functional apollo protein in the plantovule.

Thus, the present invention provides advantageous means and methods toinduce apomixis in a plant. The polynucleotides of the presentinvention, in particular those which code for a protein capable ofinducing apomixis, can be used to be transformed in a plant cell so asto produce a plant which comprises said exogenously introducedpolynucleotide, expresses said polynucleotide in a plant ovule andthereby produces an apomictic phenotype and apomictic plant. This can ina particularly preferred embodiment be achieved by using thepolynucleotides of the present invention, preferably defined in any oneof SEQ ID No. 22 to 54, preferably 23, 25, 27, 28, 29, 30, 33, 35, 37,38, 40, 41, 43, 44, 47, 50 or 53, in particular 23, 25, 28, 30, 33, 35,38, 41, 44, 47, 50 or 53, coding for a protein capable of inducingapomixis in a plant ovule, preferably defined in any one of SEQ ID No. 4to 21, preferably SEQ ID No. 4 to 9, SEQ ID No. 13 to 15 or SEQ ID No.19 to 21, under control of a constitutively expressing promoter or apromoter providing an ovule-specific expression in the ovule.

Thus, in one preferred aspect of the present invention the isolatednucleic acid molecules comprise polynucleotides, in particularpolynucleotides as specifically disclosed herein or polynucleotidevariants, for use in inducing apomixis, which code for a protein capableof inducing apomixis in a plant, in particular in a plant ovule, inparticular code for a protein with a specific exonuclease activitycapable of inducing apomixis, in particular apomeiosis, in a plantovule, and wherein said specific polynucleotides or variants thereof canadvantageously be used to be transferred into a plant, in particularplant cell, be stably integrated in its genome and can preferably beexpressed, in particular and most preferably in a constitutive manner,in the ovule of the obtained transformed plant in order to produce atransgenic apomictic plant, in particular transgenic plant, whichproduces apomictic seed. In a preferred embodiment of the presentinvention it is foreseen to transfer a polynucleotide of the presentinvention encoding a protein capable of inducing apomixis in a plant andbeing specified in any one of the consensus SEQ ID No. 1 to 9,preferably SEQ ID No. 4 to 9, most preferably SEQ ID No. 4 or 7, mostpreferably SEQ ID No. 5 or 8, most preferably SEQ ID No. 6 or 9 and inparticular as specified in any one of the specific SEQ ID No. 10 to 21,preferably SEQ ID No. 13 to 15 or 19 to 21, into a plant so as to allowexpression of said polynucleotide, preferably being under control of aconstitutively or ovule-specific promoter, thereby producing the desiredapollo protein in the ovule.

The present invention also provides polynucleotides which are capable offunctioning as a regulatory element and which can be used to transformplant cells and whereby said polynucleotides capable of functioning asregulatory elements structurally modify the regulatory elements of theendogenously present genes which code for proteins capable of inducingapomixis so as to derepress, that means activate, the endogenouslypresent regulatory elements of said genes thereby allowing theexpression of the protein capable of inducing apomixis and producingplants with an apomictic phenotype. This particular approach is based onthe findings of the present invention that the gene coding for theprotein capable of inducing apomixis is present also in wild typeplants, but is, however, not activated, that means is not induced andtherefore is not expressed in the ovule of a sexually propagating plant.Without being bound by theory, in wild type sexually propagating plantsthe expression of the endogenously present gene coding for a proteincapable of inducing apomixis is suppressed or inactivated, most likelydue to suppressed regulatory elements of the protein-coding regions.Thus, the present invention foresees in one embodiment the introductionof regulatory elements which structurally interfere with theendogenously present and suppressed regulatory elements of a nucleotidesequence region coding for a protein capable of inducing apomixis in aplant ovule allows the reversion of the suppression of the regulatoryelements and induces the expression of the coding sequence.

Accordingly, in a preferred embodiment a polynucleotide, in particular aspecifically disclosed polynucleotide or polynucleotide variant of thepresent invention, in particular a regulatory element as specified inany one of SEQ ID No. 55 to 62 or 65, is transformed into a plant so asto modify the endogenously present regulatory element having a sequenceas given in the sexual promoter given in any one of SEQ ID No. 56, 60,61 or 62 of an endogenously present gene encoding the apollo proteincapable of inducing apomixis in a plant so as to enable the expressionof the endogenously present polynucleotide encoding the polypeptidecapable of inducing apomixis in the plant, in particular the ovule.

Accordingly, the present invention provides isolated nucleic acidmolecules, which comprise polynucleotides, that means thepolynucleotides specifically disclosed herein or polynucleotidevariants, for use in inducing apomixis, wherein the specificpolynucleotides or polynucleotide variants are regulatory elements andare useful for inducing apomixis in a plant in so far as they allow aregulatable expression of coding sequences operably linked thereto inthe plant ovule, in particular during ovule development in a plant.Thus, these regulatory elements provide an ovule non-suppressability toa coding sequence and provide the advantage of being capable to directexpression of coding sequences in the ovule of plants.

Thus, in a particularly preferred embodiment an induced mutation, forinstance a recombination, duplication, deletion, insertion or inversion,of all or part of the endogenously present regulatory element for thecoding sequence of the polypeptide capable of inducing apomixis in aplant ovule allows the expression of said polynucleotide consequentlyleading to apomixis in the plant.

The present invention also allows and enables the induction of apomixisin a plant by modifying, in particular inducing, hereinafter also calledactivating, the expression of the endogenously present regulatoryelements of the endogenously present nucleotide sequence encoding aprotein capable of inducing apomixis in a plant by structurallymodifying said endogenously present regulatory elements for instance bymutating, in particular by insertion, deletion, duplication or inversionof said regulatory element. Said structural modification may preferablybe achieved by any means for mutation, for instance radiation, use ofchemical agents or of nucleotide sequences, in particular a DNAmolecule, introduced into a plant cell, which means, in particularsequence, is capable of structurally interfering with said regulatoryelement and which sequence may be a transposon or any other sequencebeing able to interfere, for instance recombine or insert into saidregulatory element in the ovule of a sexually propagating plant.

In a further embodiment, the present invention provides specificpolynucleotides and polynucleotide variants which are capable of actingas regulatory elements, in particular promoters, which very specificallyact in a regulatory manner in the ovule. In particular, in one preferredembodiment of such a regulatory element, hereinafter also called sexualpromoter, said regulatory element is capable of being expressed in allsomatic tissue of a transformed transgenic plant, but specifically notin the ovule of said plant. In another embodiment of such a regulatoryelement, hereinafter also called apo-promoter, of the present invention,said regulatory element is expressed in the somatic tissue of atransformed transgenic plant and is also expressed in the ovule of saidplant. Thus, the present invention provides polynucleotides which in oneembodiment allow a somatic gene expression excluding the ovule tissue,while in another embodiment an ovule gene expression is allowed. Saidlatter embodiment, namely the ovule expressing embodiment, beingspecified in any one of SEQ ID No. 55, 57, 58 or 59 is primarilycharacterised by a nucleotide sequence comprising a regulatory insert oftwenty nucleotides with SEQ ID No. 65 in comparison to the firstlymentioned embodiment, namely the non-ovule expressing embodiment,lacking said insert and being specified in SEQ ID No. 56, 60, 61 or 62.Thus, in a particularly preferred embodiment the regulatory element ofthe present invention allowing expression in somatic tissue, but not inthe ovule, that means the sexual promoter, is characterised by any oneof SEQ ID No. 56, 60, 61 or 62. In a furthermore preferred embodiment ofthe present invention the regulatory element capable of being expressedin the ovule, in particular by being not suppressible or not suppressed,that means the apo-promoter, is characterised by SEQ ID No. 55, 57, 58or 59.

Thus, the present invention relates in a further preferred embodiment toan isolated nucleic acid molecule, which comprises a polynucleotide,which polynucleotide is able to act as a regulatory element and isselected from the group consisting of a3) the polynucleotide defined inany one of SEQ ID No. 55 to 62 or 65, or a fully complementary strandthereof and b3) a polynucleotide variant having a degree of sequenceidentity of more than 30%, 40%, 50%, 60%, preferably 70% to the nucleicacid sequence defined in a3), or a fully complementary strand thereof,preferably wherein the sequence identity is based on the entiresequence. Preferably, the sequence identity is determined by BLASTanalysis, preferably in the NCBI database, in particular by GAP analysisusing Gap Weight of 50 and Length Weight of 3 or any other suitableanalysis.

Thus, the present invention very advantageously allows the vegetativeproduction of seed identical to the parent. In particular andpreferably, the present nucleotide acid molecules can be transformedinto a desired plant, for instance high yielding hybrids, in order tochange their reproductive mode into apomictic seed production. Thus,high yielding hybrids can according to the present invention be used inseed production to multiply identical copies of said high yieldinghybrid seed which would greatly reduce the cost for the seed productionand in turn increases the number of genotypes which could commerciallybe offered. Further on, genes can be evaluated directly in commercialhybrids, since the progeny would not segregate saving the cumbersomebackcrossing procedures. Apomixis can be used to stabilise desirablephenotypes even with complex traits such as hybrid vigor. Such traitscan be maintained very easily and be multiplied via apomixisindefinitive. Further, the present invention provides the possibility tocombine it with male sterility, advantageously preventing geneticallyengineered stabilised traits from being hybridised with undesiredrelatives.

The present invention provides a solution to the above-identifiedtechnical problem by providing specific isolated nucleic acid moleculeswhich can be used for inducing apomixis in a plant, in particular in aplant ovule, preferably for inducing apomeiosis and/or parthenogenesisin a plant, preferably in a plant ovule.

These nucleic acid molecules of the present invention comprise in onepreferred embodiment specific polynucleotides characterised by theirability to induce apomixis in a plant and by the presence of specificconsensus nucleotide sequence patterns according to any one of SEQ IDNo. 27, 28, 29, 30 or 31, in particular 27, 28, 29, 30, preferably 27 or29, which represent nucleotide patterns present in all specificallydisclosed apomixis-inducing alleles of the present invention.

In a further preferred embodiment the specific polynucleotides are thevarious apomixis-inducing alleles, which are specifically identified,isolated and characterised according to the present invention and arecharacterised in any one of SEQ ID No. 37 to 45.

The present invention is preferably characterised by providingpolynucleotides and polypeptides in specific and in consensus forms. Theconsensus forms are generalised sequence motifs, that means patterns,being in one embodiment found in all of the polymorphic apollo genesidentified and isolated according to the present invention, inparticular are common to the coding sequence of all the differentpolymorphic forms including the apomictic and sexual forms. Theconsensus sequences are also given as generalised sequence motifs solelyfound in the apomictic polymorphic alleles or, in another embodiment,are solely found in the sexual polymorphic allelic forms isolatedaccording to the present invention. The apomictic and sexual alleles canbe classified by different consensus sequences for their regulatoryelements and share the same consensus sequence for their coding regions.In the consensus sequence “Xaa” stands for any naturally occurring aminoacid and “n” for any one of the nucleotides a, t, g or c.

The specific polynucleotides and polypeptides provided in the presentinvention are specifically isolated and analysed and display theconsensus sequence pattern in exemplified form.

In a particularly preferred embodiment the present invention thereforerelates to consensus and specific polynucleotides and polypeptidescharacterised in the following tables I to III.

TABLE I Apollo-amino acid sequences (polypeptides) SEQ ID coded by SEQNo. type subtype characterisation ID No. 1 consensus Global Exonucleasedomain 26 2 consensus Apo Exonuclease domain 31 3 consensus SexExonuclease domain 36 4 consensus Global protein with duplication 22, 235 consensus Apo protein with duplication 27, 28 6 consensus Sex proteinwith duplication 32, 33 7 consensus Global protein without duplication24, 25 8 consensus Apo protein without duplication 29, 30 9 consensusSex protein without duplication 34, 35 10 specific Apo A011a Exonuclease39 domain 11 specific Apo A043a Exonuclease 42 domain 12 specific ApoA081a Exonuclease 45 domain 13 specific Apo A011a Protein 37, 38 14specific Apo A043a Protein 40, 41 15 specific Apo A081a Protein 43, 4416 specific Sex S011a Exonuclease 48 domain 17 specific Sex S355aExonuclease 51 domain 18 specific Sex S390a Exonuclease 54 domain 19specific Sex S011a Protein 46, 47 20 specific Sex S355a Protein 49, 5021 specific Sex S390a Protein 52, 53legend:

A011a, A043a, A081a: apomictic Boechera holboellii alleles; S011a,S355a, S390a: sexual Boechera holboellii alleles

“consensus” means consensus sequence, that means a general sequencemotif present in more than one specific allele of the apollo gene withspecifically identified positions for observed sequence deviations,namely nucleotide/amino acid polymorphisms. In amino acid sequences“Xaa” can be any naturally occurring amino acid. In nucleotide sequences“n” can be any of a, g, t or c, in introns “n” can additionallydesignate a missing nucleotide.

“specific” means a specifically isolated polymorphic allele withsequenced or deduced nucleotide and amino acid sequence.

“Global” means a consensus sequence both for apomictic and sexual apollogene or protein.

“Apo” means apomictic apollo gene or protein.

“Sex” means sexual apollo gene or protein.

“protein” means apollo protein.

“Exonuclease domain” means the fragment of the apollo protein in whichthe specific biologically active DEDDh 3′-5′ exonuclease activity islocated.

“duplication” means a duplicated marker sequence optionally present inthe coding region of the apomictic and sexual allele of the apollo geneand specified in SEQ ID No. 63 (amino acid) and 64 (nucleotide).

TABLE II Apollo-protein coding polynucleotides SEQ ID No. type subtypecharacterisation 22 consensus Global genomic with duplication 23consensus Global coding with duplication 24 consensus Global genomicwithout duplication 25 consensus Global coding without duplication 26consensus Global Exonuclease domain 27 consensus Apo genomic withduplication 28 consensus Apo coding with duplication 29 consensus Apogenomic without duplication 30 consensus Apo coding without duplication31 consensus Apo Exonuclease domain 32 consensus Sex genomic withduplication 33 consensus Sex coding with duplication 34 consensus Sexgenomic without duplication 35 consensus Sex coding without duplication36 consensus Sex Exonuclease domain 37 specific Apo A011a genomic 38specific Apo A011a coding 39 specific Apo A011a Exonuclease domain 40specific Apo A043a genomic 41 specific Apo A043a coding 42 specific ApoA043a Exonuclease domain 43 specific Apo A081a genomic 44 specific ApoA081a coding 45 specific Apo A081a Exonuclease domain 46 specific SexS011a genomic 47 specific Sex S011a coding 48 specific Sex S011aExonuclease domain 49 specific Sex S355a genomic 50 specific Sex S355acoding 51 specific Sex S355a Exonuclease domain 52 specific Sex S390agenomic 53 specific Sex S390a coding 54 specific Sex S390a Exonucleasedomain

legend: see table I; “genomic” means genomic DNA sequence, preferablyincluding regulatory elements, exons and introns.

“coding” means solely the coding DNA sequence which codes the fulllength apollo protein.

TABLE III Apollo-regulatory polynucleotides, peptides and inserts SEQ IDNo. type subtype characterisation 55 consensus Apo Promoter 56 consensusSex Promoter 57 specific Apo A011a promoter 58 specific Apo A043apromoter 59 specific Apo A081a promoter 60 specific Sex S011a promoter61 specific Sex S355a promoter 62 specific Sex S390a promoter 63specific Apo/Sex duplication, amino acids 64 specific Apo/Sexduplication, DNA 65 specific Apo promoter insert

legend: see table I; “promoter insert”: regulatory insertion of 20 bpfound in apo-promoters

The present invention provides in one embodiment global consensusgenomic sequences, in particular those of SEQ ID No. 22 and 24 whichrepresent nucleotide sequence patterns found in the apomictic and sexualalleles of the present invention in so far as the nucleotide sequencesgiven are to be found in both types of alleles.

Thus, in a particularly preferred embodiment of the present inventionpolynucleotides coding for the apollo protein are provided which arecharacterised by any one of the polynucleotide sequences given in SEQ IDNo. 23, 25 to 31, 33, 35 to 45, 47, 48, 50, 51, 53 or 54 which areconsensus and specific sequences found in apomictic and sexual allelesand which code for the consensus or specific apollo protein of thepresent invention of any one of SEQ ID No. 1 to 21, preferably of SEQ IDNo. 4 to 9, 13 to 15 or 19 to 21 or an essential part thereof, namelythe exonuclease domain of SEQ ID No. 1 to 3, 10 to 12 or 16 to 18. Mostpreferred are polynucleotides identified in Table I coding for theconsensus apollo proteins or essential parts thereof, namely any one ofSEQ ID No. 1 to 21, preferably 4, 5, 6, 7, 8, 9, 13, 14, 15, 19, 20 or21, in particular 4, 5, 6, 7, 8 or 9. In a preferred embodimentpolynucleotides comprising any one of SEQ ID No. 23 or 25, 26, 27, 28,29, 30, 31, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 50,51, 53 or 54 are preferred all of them comprising coding sequences forthe apollo protein, but no sexual-specific regulatory elements beingsuppressible in a plant ovule. Thus, these sequences do not comprise thesexual promoters with SEQ ID No. 56 or any one of 60, 61 and 62, whichare in particular lacking the promoter insert of SEQ ID No. 65.

However, also the polynucleotide sequences comprising sexual regulatoryelements such as the polynucleotides of SEQ ID No. 32, 34, 46, 49, 52,56, 60, 61 or 62 are preferred as comprising regulatory elements usefulfor providing suppressibility in plant ovule expression or for mutatingendogenously present apollo genes so as to induce apomixis. Thesepolynucleotides can, in a preferred embodiment, be modified, inparticular to contain the apomictic promoter insert of SEQ ID No. 65thereby resulting in a regulatory element being expressed in the ovulethereby not being suppressed anymore in the ovule of a plant.

The present invention also provides functionally equivalentpolynucleotides for use in inducing apomixis in a plant, in particularin a plant ovule, preferably for inducing apomeiosis and/orparthenogenesis in a plant, preferably in a plant ovule, which do notexactly show the specific nucleotide sequence of said specificnucleotide sequence patterns or apomixis-inducing alleles and inparticular given in the sequence identity protocols given herein, butwhich do exhibit slight deviations therefrom and which are in thecontext of the present invention termed “polynucleotide variants”. Suchpolynucleotide variants are allelic, polymorphic, mutated, truncated orprolonged variants of the polynucleotides defined in the presentsequence identity protocols and which therefore show deletions,insertions, inversions or additions of nucleotides in comparison to thepolynucleotides defined in the present sequence identity protocol. Thus,polynucleotide or polypeptide variants of the present invention,hereinafter also termed “functional equivalents” of a polynucleotide orpolypeptide, have a structure and a sufficient length to provide thesame biological activity, that means the same capability to induceapomixis in the plant as the specifically disclosed polynucleotides orpolypeptides of the present invention.

A polypeptide coded by a polynucleotide variant of the present inventionis—in case its amino acid sequence is altered in comparison to the aminoacid sequence of the polypeptide coded by the polynucleotide of thepresent invention—termed a polypeptide variant. However, due to thedegeneracy of the genetic code a polynucleotide variant not necessarilycodes in any case for a polypeptide variant but may also code apolypeptide of the present invention.

The term “variant” refers to a substantially similar sequence of thespecifically disclosed polynucleotides or polypeptides of the presentinvention. Generally, polynucleotide variants of the invention will haveat least 30%, 40%, 50%, 60%, 65%, or 70%, preferably 75%, 80% or 90%,more preferably at least 91%, preferably at least 92%, preferably atleast 93%, preferably at least 94%, preferably at least 95%, preferablyat least 96%, preferably at least 97% and most preferably at least 98%or at least 99% sequence identity to the present polynucleotides, inparticular those representing the present apomixis-inducing alleles, inparticular its coding sequence, wherein the % sequence identity is basedon the entire sequence. Preferably, the sequence identity is determinedby BLAST analysis, preferably in the NCBI database, in particular by GAPanalysis using Gap Weight of 50 and Length Weight of 3 or any othersuitable analysis.

Generally, polypeptide sequence variants of the invention will have atleast about 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75% or 80%, preferably atleast about 85% or 90%, and more preferably at least about 91%,preferably at least 92%, preferably at least 93%, preferably at least94%, preferably at least 95%, preferably at least 96%, preferably atleast 97% and most preferably at least 98% or at least 99% sequenceidentity to the present protein capable of inducing apomixis, whereinthe % sequence identity is based on the entire sequence. Preferably, thesequence identity is determined by BLAST analysis, preferably in theNCBI database, in particular by GAP analysis using Gap Weight of 12 andLength Weight of 4 or any other suitable analysis.

According to the present invention a number of amino acids of thepresent polypeptides can be replaced, inserted or deleted withoutaltering a protein's function. The relationship between proteins isreflected by the degree of sequence identity between aligned amino acidsequences of individual proteins or aligned component sequences thereof.

For sequence alignments and the determination of sequence identities inthe context of the present invention various programs and algorithms canbe used, such as the Wilbur-Lipman (Wilbur W J, Lipman D J, (1983),Rapid similarity searches of nucleic acid and protein data banks. ProcNatl Acad Sci USA 80:726-730), the Lipman-Pearson (Lipman D J, Pearson WR (1985), Rapid and sensitive protein similarity searches. Science227:1435-1441), the Martinez-NW (Needleman-Wunsch) algorithms (MartinezH (1983), An efficient method for finding repeats in molecularsequences. Nucleic Acids Res 11:4629-4634; Needleman S B and Wunsch C D(1970), A general method applicable to the search for similarities inthe amino acid sequences of two proteins. J Mol Biol 48:444-453) or acombination thereof. The Wilbur-Lipman method is preferably used withthe default ones provided by the program (ktuple=3; Gap Penalty=3;window=20). As the instructions of the program MegAlign describes, theWilbur-Lipman method constructs tables of K-tuples to find regions ofsimilarity between two DNA sequence pairs using the method of Wilbur andLipman (1983). This method reads the sequences, builds case structuresof the K-tuples, finds the diagonals and matches, and creates thefinished alignment. The method of Martinez-NW uses two alignment methodsin succession. An approach described by Martinez (Martinez H (1983), Anefficient method for finding repeats in molecular sequences. NucleicAcids Res 11:4629-4634) identifies regions of perfect match. TheNeedleman-Wunsch (Needleman S B and Wunsch C D (1970), A general methodapplicable to the search for similarities in the amino acid sequences oftwo proteins. J Mol Biol 48:444-453) method then optimizes the fit inbetween perfect matches. The conditions of the alignment were thedefault ones provided by the program (Minimum Match=9; Gap Penalty=1.10;Gap Length Penalty=0.33). The program preferably used for calculatingthe algorithms can be MegAlign (DNASTAR Lasergene version 9 Core Suite(DNASTAR, Inc., 3801 Regent Street, Madison, Wis. 53705, USA).

Dynamic programming algorithms yield different kinds of alignments.Algorithms as proposed by Needleman and Wunsch and by Sellers align theentire length of two sequences providing a global alignment of thesequences. The Smith-Waterman algorithm yields local alignments. A localalignment aligns the pair of regions within the sequences that are mostsimilar given the choice of scoring matrix and gap penalties. Thisallows a database search to focus on the most highly conserved regionsof the sequences. It also allows similar domains within sequences to beidentified. To speed up alignments using the Smith-Waterman algorithmboth BLAST (Basic Local Alignment Search Tool) and FASTA placeadditional restrictions on the alignments.

Within the context of the present invention alignments can be performedusing BLAST, a set of similarity search programs designed to explore allof the available sequence databases regardless of whether the query isprotein or DNA. Version BLAST 2.2 (Gapped BLAST) of this search tool hasbeen made publicly available (currently on the world wide web at“ncbi.nlm.nih.gov/BLAST or internet at blast.ncbi.nlm.nih.gov. It uses aheuristic algorithm which seeks local as opposed to global alignmentsand is therefore able to detect relationships among sequences whichshare only isolated regions. The scores assigned in a BLAST search havea well-defined statistical interpretation. Particularly useful withinthe scope of the present invention are the blastp program allowing forthe introduction of gaps in the local sequence alignments and thePSI-BLAST program, both programs comparing an amino acid query sequenceagainst a protein sequence database, as well as a blastp variant programallowing local alignment of two sequences only.

Sequence alignments, preferably using BLAST, can also take into accountwhether the substitution of one amino acid for another is likely toconserve the physical and chemical properties necessary to maintain thestructure and function of a protein or is more likely to disruptessential structural and functional features. For examplenon-conservative replacements may occur at a low frequency andconservative replacements may be made between amino acids within thefollowing groups: (i) serine and threonine; (ii) glutamic acid andaspartic acid; (iii) arginine and lysine; (iv) asparagine and glutamine;(v) isoleucine, leucine, valine and methionine; (vi) phenylalanine,tyrosine and tryptophan (vii) alanine and glycine.

Such sequence similarity is quantified in terms of percentage ofpositive amino acids, as compared to the percentage of identical aminoacids.

The polynucleotide or polypeptide variants of the present invention,however, are in spite of their structural deviations also capable ofexhibiting the same or essentially the same biological activity as thepolynucleotides or polypeptides defined in the sequence identityprotocols of the present invention.

In the context of the present invention the term “biological activity”refers to the capability of the polynucleotide or polypeptide of thepresent invention or their variants to induce apomixis in a plant. Theterm “to induce apomixis in a plant” refers to the capability of apolynucleotide or polypeptide or variant thereof to induce an asexualproduction of viable seed in a plant, in particular in the ovule of aplant, in particular the capability to induce apomeiosis orparthenogenesis or both apomeiosis and parthenogenesis in a plant ovule,in particular by coding or exerting an exonuclease activity in theovule.

In one embodiment of the present invention a polynucleotide of thepresent invention is able to induce apomixis in a plant ovule byactivating or derepressing, in particular by structurally changing, aregulatory element of an endogenously present gene coding for a proteinwith an ovule exonuclease activity, preferably ovule-specificexonuclease activity, capable of inducing apomixis in a plant. Such agene is in particular characterised by having a polynucleotide sequenceaccording to the present invention and thereby allowing, uponderepression, that means induction, the expression of said endogenouslycoded protein with an ovule exonuclease activity, preferably anovule-specific exonuclease activity, capable of inducing apomixis in theplant.

In a particularly preferred embodiment the biological activity exertedby a polypeptide of the present invention, that means a protein capableof inducing apomixis in a plant, is a specific exonuclease activitycharacterised by expression at least in the ovule, preferably by anovule specificity, in so far as its expression is activated in theovule, preferably specifically in the ovule, of an apomictic plant andrepressed or inactivated in a sexual plant.

In particular, the present protein, namely the apollo protein, which iscapable of inducing apomixis in a plant, in particular a plant ovule andhaving a specific exonuclease activity appears to be, without beingbound by theory, a DEDD 3′→5′ exo-nuclease, also termed a DNA Q protein,which preferably is characterised by four acidic residues, namely threeaspartats (D) and glutamate (E) distributed in three separate sequencesegments, namely exo I, exo II and exo III (Moser et al., Nucl. Acids.Res 25 (1997), 5110-5118). Furthermore, these proteins are characterisedby either a tyrosine (y) or histidine (h) amino acid located at itsactive side determinative for being a DEDDy or DEDDh protein. In apreferred embodiment, the present polypeptide capable of inducingapomixis in a plant ovule is a DEDDh exonuclease, preferably comprisingthe amino acid sequence as given in any one of SEQ ID No. 1 to 3, 10 to12 or 16 to 18, preferably catalysing the excision of nucleosidemonophosphates at the DNA or RNA termini in the 3′-5′ direction. Inparticular, the present exonuclease is a plant DEDDh exonuclease.

In a particularly preferred embodiment the specific biological activityperformed by the polypeptide capable of inducing apomixis in the plantovule in said plant ovule, that means the apollo protein, appears to bea meiosis-modifying, in particular meiosis-altering, changing or varyingactivity, in particular is a meiosis-inhibiting activity therebypreventing the reduction of chromosome number in the germ cells.

The isolated nucleic acid molecules of the present invention may bepresent in isolated form. The isolated nucleic acid molecules of thepresent invention may, however, also be combined with other nucleic acidmolecules, for instance regulatory elements or vectors, thereby forminganother molecule comprising not solely the nucleic acid molecule of thepresent invention. In this case the “nucleic acid molecule” of thepresent invention is also termed a “nucleic acid sequence” of thepresent invention.

In the context of the present invention the term “comprising” isunderstood to have the meaning of “including” or “containing” whichmeans that one first entity contains a second entity, wherein said firstentity may in addition to the second entity further contain a thirdentity. Thus, in particular, the term “a nucleic acid moleculecomprising a polynucleotide” means that the nucleic acid molecule of thepresent invention contains a polynucleotide or a polynucleotide variantof the present invention, but may in addition contain other nucleotidesor polynucleotides. In a particular preferred embodiment the term“comprising” as used herein is also understood to mean “consisting of”thereby excluding the presence of other elements besides the explicitlymentioned element. Thus, the present invention also relates to nucleicacid molecules which consist of polynucleotides or polynucleotidevariants of the present invention, meaning that the nucleic acidmolecule is only composed of the polynucleotide or polynucleotidevariant of the present invention and does not comprise any furthernucleotides, polynucleotides or other elements. According to thisembodiment, the nucleic acid molecule of the present invention is thepolynucleotide or polynucleotide variant of the present invention.

Both, the nucleic acid molecule of the present invention and thepolynucleotide comprised therein do exhibit the desired biologicalactivity of being capable of inducing apomixis.

The term “apomixis” refers to the replacement of the normal sexualreproduction by asexual reproduction, that means preferably reproductionwithout fertilisation of the egg cell, in particular that means onlyfertilisation of the central cell which is a pseudogamous event, inparticular without any fertilisation, in particular the term refers toasexual reproduction through seeds, leading to apomictically producedoff-springs or progeny genetically identical to the parent plant, inparticular the female plant.

The term “gene” refers to a coding nucleotide sequence and associatedregulatory nucleotide sequences. The coding sequence is transcribed intoRNA, which depending on the specific gene, will be mRNA, rRNA, tRNA,snRNA, sense RNA or antisense RNA. Examples of regulatory sequences,hereinafter also termed regulatory elements, are promoter sequences, 5′and 3′ untranslated sequences and termination sequences. Furtherelements that may be present are, for example, introns or enhancers. Astructural gene may constitute an uninterrupted coding region or it mayinclude one or more introns bounded by appropriate splice junctions. Thestructural gene may be a composite of segments derived from differentsources, naturally occurring or synthetic.

The gene to be expressed may be modified in that known mRNA instabilitymotifs or polyadenylation signals are removed or codons which arepreferred by the plant into which the sequence is to be inserted may beused.

The present invention also relates to the present nucleic acidmolecules, in particular a polynucleotide or polynucleotide variant ofthe present invention, in particular a DNA sequence, wherein saidnucleic acid molecule or sequence encodes a polypeptide capable ofinducing apomixis, in particular in a plant, preferably plant ovule, andhaving, preferably comprising, the amino acid sequence depicted in SEQID No. 1, 2, 3, 10, 11, 12, 16, 17 or 18, or a polypeptide variantthereof, that means a functional equivalent of a polypeptide of thepresent invention, preferably a polypeptide being in terms of biologicalactivity similar thereto. The present invention, thus, also provides apolypeptide variant of the present invention, in particular having alength of at least 150, at least 200, at least 250, at least 300, atleast 350, at least 400, at least 450, at least 500 amino acids whichafter alignment reveals at least 30% or 40% and preferably at least 50%,at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, atleast 99% or more sequence identity with the, preferably full-length,polypeptide of the present invention, in particular as characterised inany one of SEQ ID No. 1 to 21, preferably 4, 5, 6, 7, 8, 9, 13, 14, 15,19, 20 or 21.

The terms “protein” and “polypeptide” are used interchangeably and referto a molecule with a particular amino acid sequence comprising at least20, 30, 40, 50 or 60 amino acid residues.

The term “polypeptide” thus means proteins of the present invention andvariants thereof, in particular protein fragments, modified proteins,amino acid sequences and synthetic amino acid sequences. According tothe present invention the polypeptide can be glycosylated or not.

A polypeptide variant of the present invention which is truncated isalso termed a “fragment” of the present invention. Thus, the term“fragment” refers to a portion of a polynucleotide sequence or a portionof a polypeptide, that means an amino acid sequence of the presentinvention and hence polypeptide encoded thereby. Fragments of apolynucleotide sequence such as SEQ ID No. 26, 31, 36, 39, 42, 45, 48,51 or 54, may encode polypeptide fragments that retain the biologicalactivity of the polypeptide of the present invention, such as given inany one of SEQ ID No. 1, 2, 3, 10, 11, 12, 16, 17 or 18. Alternatively,fragments of a polynucleotide sequence that are useful as hybridizationprobes generally do not encode fragments of a polypeptide retainingbiological activity. Fragments of a polynucleotide sequence aregenerally greater than 20, 30, 50, 100, 150, 200 or 300 nucleotides andup to the entire nucleotide sequence encoding the polypeptide of thepresent invention. Generally, the fragments have a length of less than1000 nucleotides and preferably less than 500 nucleotides. Fragments ofthe invention include antisense sequences used to decrease expression ofthe present polynucleotides. Such antisense fragments may vary in lengthranging from at least 20 nucleotides, 50 nucleotides, 100 nucleotides,up to and including the entire coding sequence.

The term “regulatory element” refers to a sequence, preferably anucleotide sequence, located upstream (5′), within and/or downstream(3′) to a nucleotide sequence, preferably a coding sequence, whosetranscription and expression is controlled by the regulatory element,potentially in conjunction with the protein biosynthetic apparatus ofthe cell. “Regulation” or “regulate” refer to the modulation of the geneexpression induced by DNA sequence elements located primarily, but notexclusively upstream (5′) from the transcription start of the gene ofinterest. Regulation may result in an all or none response to astimulation, or it may result in variations in the level of geneexpression.

A regulatory element, in particular DNA sequence, such as a promoter issaid to be “operably linked to” or “associated with” a DNA sequence thatcodes for a RNA or a protein, if the two sequences are situated andorientated such that the regulatory DNA sequence effects expression ofthe coding DNA sequence.

A “promoter” is a DNA sequence initiating transcription of an associatedDNA sequence, in particular being located upstream (5′) from the startof transcription and being involved in recognition and being of theRNA-polymerase. Depending on the specific promoter region it may alsoinclude elements that act as regulators of gene expression such asactivators, enhancers, and/or repressors.

A “3′ regulatory element” (or “3′ end”) refers to that portion of a genecomprising a DNA segment, excluding the 5′ sequence which drives theinitiation of transcription and the structural portion of the gene, thatdetermines the correct termination site and contains a polyadenylationsignal and any other regulatory signals capable of effecting messengerRNA (mRNA) processing or gene expression. The polyadenylation signal isusually characterised by effecting the addition of polyadenylic acidtracts to the 3′ end of the mRNA precursor. Polyadenylation signals areoften recognised by the presence of homology to the canonical form5′-AATAAA-3′.

The term “coding sequence” refers to that portion of a gene encoding aprotein, polypeptide, or a portion thereof, and excluding the regulatorysequences which drive the initiation or termination of transcription.

The gene, coding sequence or the regulatory element may be one normallyfound in the cell, in which case it is called “autologous”, or it may beone not normally found in a cellular location, in which case it istermed “heterologous” or “transgenic”.

A “heterologous” gene, coding sequence or regulatory element may also beautologous to the cell but is, however, arranged in an order and/ororientation or in a genomic position or environment not normally foundor occurring in the cell in which it is transferred.

The term “vector” refers to a recombinant DNA construct which may be aplasmid, virus, autonomously replicating sequence, an artificialchromosome, such as the bacterial artificial chromosome BAC, phage orother nucleotide sequence, in which at least two nucleotide sequences,at least one of which is a nucleic acid molecule of the presentinvention, have been joined or recombined. A vector may be linear orcircular. A vector may be composed of a single or double stranded DNA orRNA. A vector may be derived from any source. Such a vector ispreferably capable of introducing the regulatory element, for instance apromoter fragment, and the nucleic acid molecule of the presentinvention, preferably a DNA sequence for inducing apomixis, in a plant,in sense or antisense orientation along with appropriate 3′ untranslatedsequence into a cell, in particular a plant cell.

The term “expression” refers to the transcription and/or translation ofan endogenous gene or a transgene in plants.

“Marker genes” usually encode a selectable or screenable trait. Thus,expression of a “selectable marker gene” gives the cell a selectiveadvantage which may be due to their ability to grow in the presence of anegative selective agent, such as an antibiotic or a herbicide comparedto the growth of non-transformed cells. The selective advantagepossessed by the transformed cells, compared to non-transformed cells,may also be due to their enhanced or novel capacity to utilize an addedcompound as a nutrient, growth factor or energy source. Selectablemarker gene also refers to a gene or a combination of genes whoseexpression in a plant cell gives the cell both, a negative and apositive selective advantage. On the other hand a “screenable markergene” does not confer a selective advantage to a transformed cell, butits expression makes the transformed cell phenotypically distinct fromuntransformed cells.

The term “expression in the vicinity of the embryo sac” refers toexpression in carpel, integuments, ovule, ovule primordium, ovary wall,chalaza, nucellus, funicle or placenta. The term “integuments” refers totissues which are derived therefrom, such as endothelium. The term“embryogenic” refers to the capability of cells to develop into anembryo under permissive conditions.

The term “plant” refers to any plant, but particularly seed plants.

The term “transgenic plant” or “transgenic plant cell” or “transgenicplant material” refers to a plant, plant cell or plant material which ischaracterised by the presence of a polynucleotide or polynucleotidevariant of the present invention, which may—in case it is autologous tothe plant—either be located at another place or in another orientationthan usually found in the plant, plant cell or plant material or whichis heterologous to the plant, plant cell or plant material. Preferably,the transgenic plant, plant cell or plant material expresses thepolynucleotide or its variants such as to induce apomixis.

A transgenic plant, transgenic plant cell or transgenic plant materialcan be identified at the phenotypical level, for instance by observationof apomictic seed production, or at protein level, for instance byimmunodetection or at the DNA or RNA level, for instance with polymerasechain reaction (PCR). Even in case the transgene in the transgenicplant, transgenic plant cell or transgenic plant material has a naturalhomologue therein with a very high similarity, PCR can be used todiscriminate such a transgene by at least one nucleotide difference. Inparticular, SNP (single nucleotide polymorphism) existing between hostalleles and transforming alleles can be used to detect transformedplants simply by PCR.

The term “plant cell” describes the structural and physiological unit ofthe plant, and comprises a protoplast and a cell wall. The plant cellmay be in form of an isolated single cell, such as a stomatal guardcells or a cultured cell, or as a part of a higher organized unit suchas, for example, a plant tissue, or a plant organ.

The term “plant material” includes plant parts, in particular plantcells, plant tissue, in particular plant propagation material,preferably leaves, stems, roots, emerged radicles, flowers or flowerparts, petals, fruits, pollen, pollen tubes, anther filaments, ovules,embryo sacs, egg cells, ovaries, zygotes, embryos, zygotic embryos perse, somatic embryos, hypocotyl sections, apical meristems, vascularbundles, pericycles, seeds, roots, cuttings, cell or tissue cultures, orany other part or product of a plant.

Thus, the present invention also provides plant propagation material ofthe transgenic plants of the present invention. Said “plant propagationmaterial” is understood to be any plant material that may be propagatedsexually or asexually in vivo or in vitro. Particularly preferred withinthe scope of the present invention are protoplasts, cells, calli,tissues, organs, seeds, embryos, pollen, egg cells, zygotes, togetherwith any other propagating material obtained from transgenic plants.Parts of plants, such as for example flowers, stems, fruits, leaves,roots originating in transgenic plants or their progeny previouslytransformed by means of the methods of the present invention andtherefore consisting at least in part of transgenic cells, are also anobject of the present invention. Especially preferred plant materials,in particular plant propagation materials, are apomictic seeds.

Particularly preferred plants are monocotyledonous or dicotyledonousplants. Particularly preferred are crop or agricultural plants, such assunflower, peanut, corn, potato, sweet potato, bean, pea, chicory,lettuce, endive, cabbage, cauliflower, broccoli, turnip, radish,spinach, onion, garlic, eggplant, celery, carrot, squash, pumpkin,zucchini, cucumber, apple, pear, melon, strawberry, grape, raspberry,pineapple, soybean, Cannabis, Humulus (hop), tomato, sorghum, sugarcane, and non-fruit bearing trees such as poplar, rubber, Paulownia,pine, elm, Lolium, Festuca, Dactylis, alfalfa, safflower, tobacco,cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea, banana,avocado, fig, guava, mango, olive, papaya, cashew, macadamia, almond,green beans, lima beans, peas, fir, hemlock, spruce, redwood, inparticular maize, wheat, barley, sorghum, rye, oats, turf and foragegrasses, millet, rice and sugar cane. Especially preferred are maize,wheat, sorghum, rye, oats, turf grasses and rice.

Particularly preferred are also ornamental plants such as ornamentalflowers and ornamental crops, for instance Begonia, Carnation,Chrysanthemum, Dahlia, Gardenia, Asparagus, Geranium, Daisy, Gladiolus,Petunia, Gypsophila, Lilium, Hyacinth, Orchid, Rose, Tulip, Aphelandra,Aspidistra, Aralia, Clivia, Coleus, Cordyline, Cyclamen, Dracaena,Dieffnbachia, Ficus, Philodendron, Poinsettia, Fern, Ivy, Hydrangea,Limonium, Monstera, Palm, Date-palm, Potho, Singonio, Violet, Daffodil,Lavender, Lily, Narcissus, Crocus, Iris, Peonies, Zephyranthes,Anthurium, Gloxinia, Azalea, Ageratum, Bamboo, Camellia, Dianthus,Impatien, Lobelia, Pelargonium, Lilac, Lily of the Valley, Stephanotis,Hydrangea, Sunflower, Gerber daisy, Oxalis, Marigold and Hibiscus.

Among the dicotyledonous plants Arabidopsis, Boechera, soybean, cotton,sugar beet, oilseed rape, tobacco, pepper, melon, lettuce, Brassicavegetables, in particular Brassica napus, sugar beet, oilseed rape andsunflower are more preferred herein.

“Transformation”, “transforming” and “transferring” refers to methods totransfer nucleic acid molecules, in particular DNA, into cellsincluding, but not limited to, biolistic approaches such as particlebombardment, microinjection, permeabilising the cell membrane withvarious physical, for instance electroporation, or chemical treatments,for instance polyethylene glycol or PEG, treatments; the fusion ofprotoplasts or Agrobacterium tumefaciens or rhizogenes mediatedtrans-formation. For the injection and electroporation of DNA in plantcells there are no specific requirements for the plasmids used. Plasmidssuch as pUC derivatives can be used. If whole plants are to beregenerated from such transformed cells, the use of a selectable markeris preferred. Depending upon the method for the introduction of desiredgenes into the plant cell, further DNA sequences may be necessary; if,for example, the Ti or Ri plasmid is used for the transformation of theplant cell, at least the right border, often, however, the right andleft border of the Ti and Ri plasmid T-DNA have to be linked as flankingregion to the genes to be introduced. Preferably, the transferrednucleic acid molecules are stably integrated in the genome or plastomeof the recipient plant.

The expression “progeny” or “offspring” refers to both, “asexually” and“sexually” generated progeny of transgenic plants. This definition isalso meant to include all mutants and variants obtainable by means ofknown processes, such as for example cell fusion or mutant selection andwhich still exhibit the characteristic properties of the initialtransformed plant of the present invention, together with all crossingand fusion products of the transformed plant material. This alsoincludes progeny plants that result from a backcrossing, as long as thesaid progeny plants still contain the polynucleotide and/or polypeptideaccording to the present invention.

The isolated nucleic acid molecule of the present invention ispreferably a DNA, preferably a DNA from a plant, preferably fromBrassicaceae, in particular Boechera, in particular Boechera holboellii,Boechera divaricarpa or Boechera stricta, in a particular genomic orcDNA sequence molecule. It may, however, also be a RNA, in particularmRNA.

The present invention also provides in a preferred embodiment a vectorcomprising the nucleic acid sequence according to the present invention.Both, the specific polynucleotide or the polynucleotide variant of thepresent invention can be contained in the vector in sense or antisenseorientation to a regulatory element.

In a preferred embodiment the vector comprises the nucleic acid sequenceof the present invention, in particular the specific polynucleotide orits variant coding the apomixis-inducing protein of the presentinvention, operably linked to at least one regulatory element, forinstance a promoter, enhancer and/or polyadenylation signal.

In a preferred embodiment, said promoter is an inducible or constitutivepromoter. The promoter may be a regulatable promoter. The promoter mayalso be an ovule-specific promoter, which is a promoter allowing theexpression of an operably linked coding sequence in the plant ovule of aplant, but not in other plant tissues.

In a preferred embodiment, the promoter is the Ubiquitin-, ocs-, mas-,actin-, ADH-, NOS- or CaMV355-promoter. In order to obtain expression ofthe present nucleic acid molecule in a regenerated plant, in particularthe ovule thereof, in a tissue specific manner the polynucleotide orpolynucleotide variant of the present invention is preferably underexpression control a regulatory element, for instance of an inducible ordevelopmentally regulated promoter.

In a furthermore preferred embodiment of the present invention thepolynucleotide, in particular the specific polynucleotide orpolynucleotide variant, coding for a protein with exonuclease activityis operably linked to a polynucleotide or polynucleotide variant of thepresent invention which is able to act as a regulatory element, inparticular a promoter.

In a furthermore preferred embodiment of the present invention thevector comprises a polynucleotide, in particular the specificpolynucleotide or polynucleotide variant of the present inventioncapable of acting as a regulatory element operably linked to a proteincoding nucleic acid sequence desired to be expressed in a plant, inparticular a plant ovule.

The present invention also provides in a preferred embodiment a hostcell containing the vector of the present invention. Preferably, thehost cell is not a human cell, preferably not a human stem cell,germinal cell or embryogenic cell.

The present invention also provides a transgenic plant, plant cell,plant material, in particular plant seed comprising at least one nucleicacid molecule according to the present invention or the vector of thepresent invention. The present invention also provides in a preferredembodiment a cell culture, preferably a plant cell culture comprising acell according to the present invention.

In a particularly preferred embodiment the present invention provides atransgenic plant, plant cell, plant material, in particular plant seed,wherein the polynucleotide, the polypeptide or the variant thereofexhibit its biological function. In a particular embodiment of thepresent invention a plant or plant seed is provided which comprises thepolynucleotide, polypeptide or variants thereof of the present inventionand which show due to the presence of said polynucleotide or polypeptideor variant thereof apomixis.

The present invention also provides proteins, in particular polypeptidesor polypeptides variants, that means functional equivalents topolypeptides of the present invention, that means polypeptides capableof inducing apomixis in a plant or in vitro, which are coded by thenucleic acid molecules of the present invention.

Thus, in a particularly preferred embodiment of the present inventionthe present proteins capable of inducing apomixis in a plant are apolloproteins, that means comprise an amino acid sequence as characterised byany one of SEQ ID No. 1 to 21, preferably 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20 or 21, preferably 4, 5, 6, 7, 8, 9, 13,14, 15, 19, 20 or 21, preferably 4, 5, 6, 7, 8 or 9. In a particularlypreferred embodiment the present proteins capable of inducing apomixisin a plant have, preferably comprise, an amino acid sequence as setforth in any one of SEQ ID No. 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20 or 21, preferably 13, 14, 15, 19, 20 or 21. Preferred are alsoproteins comprising the amino acid sequence as given in SEQ ID No. 1, 2or 3.

The present invention also provides a method for inducing apomixis in aplant, wherein the expression of a nucleotide sequence encoding aprotein capable of inducing apomixis in the plant, in particular theapollo protein, in particular in the ovule of the plant, is induced insaid ovule. Most preferably, said protein has, preferably comprises, theamino acid sequence as specified in any one of SEQ ID No. 1 to 21,preferably 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20or 21, preferably 4 to 9, 13 to 15 or 19 to 21, preferably 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20 or 21, most preferably 4, 5, 6, 7, 8 or9, in particular 1, 2 or 3.

Thus, the present invention foresees a method according to which in aplant ovule the expression of the polynucleotides of the presentinvention, in particular the presence of the protein of the presentinvention capable of inducing apomixis, is provided in order to induceapomixis and whereby said polynucleotides either have been transformedin said plant in an expressible status, that means in a form capable ofinducing apomixis, or are endogenously present and are activated, inparticular their regulatory elements, by mutation, for instance byradiation, chemical agents or exogenously transformed polynucleotides.Thus, the present invention provides the teaching to induce theexpression of polynucleotides of the present invention in the plantovule so as to allow the induction of apomixis in the plant ovule.

In a particularly preferred embodiment of the present invention thepresent invention therefore foresees to induce expression ofpolynucleotides encoding polypeptides capable of inducing apomixis in aplant ovule by transforming a plant with polynucleotides of the presentinvention being under appropriate regulatory control, in particularunder control of a promoter, which polynucleotide codes a proteincapable of inducing apomixis in a plant, so as to allow and induceexpression of the transformed polynucleotide in the plant ovule therebyinducing apomixis in the plant.

The present invention also provides a method for inducing apomixis in aplant by transforming a plant cell with the isolated nucleic acidmolecule according to the present invention or the vector according tothe present invention and regenerating the transformed plant cell into atransformed plant that contains, in particular contains and expresses,the at least one nucleic acid sequence of the present invention so as toinduce apomixis in the plant.

The present invention also provides a method for inducing apomixis in aplant, wherein the regulation of endogenously present polynucleotideshaving the same DNA sequence as the presently isolated polynucleotidesof the present invention are induced to be expressed in a plant ovule.Thus, in this preferred embodiment, the present invention teaches toinduce the expression of endogenously present polynucleotides encodingproteins capable of inducing apomixis in a plant ovule, in particular bystructurally altering the regulatory elements of said endogenouslypresent polynucleotide sequence, in particular its promoter, so as toallow expression therefrom.

The present invention achieves said structurally altering of theregulatory elements of said endogenously present polynucleotide sequencecoding a protein capable of inducing apomixis in the plant bytransforming the plant with either any DNA sequence capable ofstructurally modifying the endogenously present regulatory elements ofsaid polynucleotide capable of expressing a protein capable of inducingapomixis in a plant or by transforming the specific regulatory elementsof the present invention so as to induce apomixis in the plant.

Thus, the present invention also relates to a method for the productionof an apomictic plant by transforming a plant cell with the isolatednucleic acid molecule or the vector of the present invention andregenerating the transformed plant cell into a transformed plant thatcontains, in particular contains and expresses, the at least one nucleicacid sequence of the present invention so as to induce apomixis in theplant.

The present invention also provides a method of inducing vegetativereproduction via seeds in a plant generation comprising transforming aplant cell with the isolated nucleic acid molecule according to thepresent invention or the vector according to the present invention andregenerating the transformed plant cell into a transformed plant whichcontains, in particular contains and expresses, the at least one nucleicacid sequence so as to induce apomixis in the plant.

The present invention also provides a method for inducing apomixis, inparticular for inducing vegetative reproduction of a new or furtherplant generation, comprising transgenically expressing a nucleic acidmolecule, in particular nucleic acid sequence of the present invention,in particular in a plant or plant cell.

In a particularly preferred embodiment of the present invention thenucleic acid sequence of the present invention, in particular thetransgenic polynucleotide or polynucleotide variant of the presentinvention, is transgenically expressed in the ovule, in particularvicinity of the embryo sac.

The present invention also provides in a preferred embodiment a methodfor isolating an apomixis-inducing nucleic acid molecule from a plantwherein the isolated nucleic acid molecule of the present invention isused to screen and isolate nucleic acid molecules derived from theplant. Thus, the present invention provides the teaching on the identityof a nucleic acid molecule for use in inducing apomixis in plants whichallows the skilled person to design on the basis of said nucleic acidmolecules one or more primer to identify similar sequence by PCR in agenome or a part thereof.

The present invention also relates in a preferred embodiment to a methodfor identifying, in particular screening, for an effector of apomixis,in particular an apomictic phenotype, wherein a transgenic plant, plantcell or plant material according to the present invention is used, inparticular cultivated, preferably cultivated and analysed.

Apomixis effectors can be detected by different technologies, preferablydepending upon the initial information available, for instance byprotein or immunodetection.

Thus, the present invention also provides means and methods to identifyand obtain further substances, in particular proteins or nucleic acidsequences, which are involved in the development of an apomicticphenotype, in particular which are associated, in particular relate tothe development of an apomictic phenotype.

Whilst the present invention is particularly described by way of theproduction of apomictic seed by heterologous expression of apolynucleotide of the present invention, it will be recognized thatvariants of the present polynucleotides, the products of which have asimilar structure and function may likewise be expressed with similarresults. Moreover, although the example illustrates apomictic seedproduction in Boechera and Arabidopsis, the invention is, of course, notlimited to the expression of apomictic seed-inducing genes solely inthese plants. Moreover, the present disclosure also includes thepossibility of expressing the inventive polynucleotides in transformedplant material in a constitutive, tissue non-specific manner, forexample under transcriptional control of a Ubiquitin-, ocs-, mas-,actin-, ADH-, CaMV35S or NOS promoter.

The following embodiments represent particularly preferred variants ofthe present invention.

Embodiment 1: A method for inducing apomixis in a plant, wherein anucleotide sequence encoding a protein capable of inducing apomixis in aplant is induced to be expressed in the ovule of said plant and whereinsaid nucleotide sequence comprises a polynucleotide, which codes for aprotein with exonuclease activity, which polynucleotide is selected fromthe group consisting of

-   xa) the polynucleotide defined in any one of SEQ ID No. 22 to 54 or    a fully complementary strand thereof,-   xb) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 1 to 21 or a fully    complementary strand thereof, and-   xc) a polynucleotide variant having a degree of sequence identity of    more than 30%, 40%, 50% or preferably 70% to the nucleic acid    sequence defined in xa) or xb), or a fully complementary strand    thereof.

Embodiment 2: The method of embodiment 1, wherein the polynucleotide isselected from the group consisting of

-   xa1) the polynucleotide defined in any one of SEQ ID No. 26, 31, 36,    39, 42, 45, 48, 51, 54 or a fully complementary strand thereof,-   xb1) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 1, 2, 3, 10, 11, 12, 16,    17, 18 or a fully complementary strand thereof, and-   xc1) a polynucleotide variant having a degree of sequence identity    of more than 30%, 40%, 50% or, preferably 70% to the nucleic acid    sequence defined in xa1) or xb1), or a fully complementary strand    thereof.

Embodiment 3: The method of embodiment 1, wherein the polynucleotide isselected from the group consisting of

-   xa2) the polynucleotide defined in any one of SEQ ID No. 22, 23, 27,    28, 32, 33 or a fully complementary strand thereof,-   xb2) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 4, 5, 6 or a fully    complementary strand thereof, and-   xc2) a polynucleotide variant having a degree of sequence identity    of more than 70% to the nucleic acid sequence defined in xa2) or    xb2), or a fully complementary strand thereof.

Embodiment 4: An isolated nucleic acid molecule for use in inducingapomixis in a plant, which comprises a polynucleotide whichpolynucleotide is able to act as a regulatory element and is selectedfrom the group consisting of

-   a3) the polynucleotide defined in any one of SEQ ID No. 55 to 62 or    65 or a fully complementary strand thereof and-   b3) a polynucleotide variant having a degree of sequence identity of    more than 70% to the nucleic acid sequence defined in a3), or a    fully complementary strand thereof.

Embodiment 5: An isolated nucleic acid molecule for use in inducingapomixis in a plant, which comprises a polynucleotide coding for aprotein with exonuclease activity, which polynucleotide is selected fromthe group consisting of

-   xa4) the polynucleotide defined in any one of SEQ ID No. 26, 31, 36,    39, 42, 45, 48, 51, 54 or a fully complementary strand thereof,-   xb4) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 1, 2, 3, 10, 11, 12, 16,    17, 18 or a fully complementary strand thereof, and-   xc4) a polynucleotide variant having a degree of sequence identity    of more than 98% to the nucleic acid sequence defined in xa4) or    xb4), or a fully complementary strand thereof.

Embodiment 6: An isolated nucleic acid molecule for use in inducingapomixis in a plant, which comprises a polynucleotide coding for aprotein with exonuclease activity, which polynucleotide is selected fromthe group consisting of

-   xa5) the polynucleotide defined in any one of SEQ ID No. 22, 23, 24,    25, 27, 28, 29, 30, 32, 33, 34, 35, 37, 38, 40, 41, 43, 44, 46, 47,    49, 50, 52, 53 or a fully complementary strand thereof,-   xb5) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 4, 5, 6, 7, 8, 9, 13, 14,    15, 19, 20, 21 or a fully complementary strand thereof, and-   xc5) a polynucleotide variant having a degree of sequence identity    of more than 90% to the nucleic acid sequence defined in xa5) or    xb5), or a fully complementary strand thereof.

Embodiment 7: A vector comprising the nucleic acid molecule of any oneof embodiments 4 to 6.

Embodiment 8: A host cell containing the vector of embodiment 7.

Embodiment 9: A protein encoded by a nucleotide acid sequence accordingto any one of embodiments 5 or 6.

Embodiment 10: A transgenic plant, plant cell or plant materialcomprising at least one transgenic nucleic acid molecule of any one ofembodiments 4 to 6 or the vector of embodiment 7.

Embodiment 11: A cell culture, preferably a plant cell culturecomprising a cell according to embodiment 8.

Embodiment 12: The method for inducing apomixis in a plant according toany one of embodiments 1 to 3, wherein the expression is induced bytransforming a plant cell with an isolated nucleic acid moleculecomprising a polynucleotide which codes for a protein with exonucleaseactivity as defined in any one of embodiments 1 to 3, 5 or 6, with theisolated nucleic acid molecule of embodiment 4 or with the vectoraccording to embodiment 7 and regenerating the transformed plant cellinto a transformed plant that contains the transformed at least onenucleic acid sequence so as to induce apomixis in the plant.

Embodiment 13: A method for the production of an apomictic plant,wherein a plant cell is transformed with a nucleic acid molecule capableof inducing the expression of a nucleotide sequence encoding a proteincapable of inducing apomixis in a plant and regenerating the transformedplant cell into a transformed plant that contains the transformednucleic acid molecule so as to induce apomixis in the plant, wherein thenucleotide sequence encoding the protein capable of inducing apomixis inthe plant is a polynucleotide, which codes for a protein withexonuclease activity, which polynucleotide is selected from the groupconsisting of

-   xa) the polynucleotide defined in any one of SEQ ID No. 22 to 54 or    a fully complementary strand thereof,-   xb) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 1 to 21 or a fully    complementary strand thereof, and-   xc) a polynucleotide variant having a degree of sequence identity of    more than 70% to the nucleic acid sequence defined in xa) or xb), or    a fully complementary strand thereof.

Embodiment 14: The method for the production of an apomictic plant bytransforming according to embodiment 13, wherein the plant cell istransformed with an isolated nucleic acid molecule comprising apolynucleotide, which codes for a protein with exonuclease activity,which polynucleotide is selected from the group consisting of

-   xa) the polynucleotide defined in any one of SEQ ID No. 22 to 54 or    a fully complementary strand thereof,-   xb) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 1 to 21 or a fully    complementary strand thereof, and-   xc) a polynucleotide variant having a degree of sequence identity of    more than 70% to the nucleic acid sequence defined in xa) or xb), or    a fully complementary strand thereof-   or with the isolated nucleic acid molecule of embodiment 4 or with    the vector of embodiment 7 and the transformed plant cell is    regenerated into a transformed plant that contains the at least one    nucleic acid sequence so as to induce apomixis in the plant.

Embodiment 15: A method for isolating an apomixis inducing nucleic acidmolecule from a plant, wherein an isolated nucleic acid moleculecomprising a polynucleotide, which codes for a protein with exonucleaseactivity, which polynucleotide is selected from the group consisting of

-   xa) the polynucleotide defined in any one of SEQ ID No. 22 to 54 or    a fully complementary strand thereof,-   xb) a polynucleotide encoding a polypeptide with the amino acid    sequence defined in any one of SEQ ID No. 1 to 21 or a fully    complementary strand thereof, and-   xc) a polynucleotide variant having a degree of sequence identity of    more than 70% to the nucleic acid sequence defined in xa) or xb), or    a fully complementary strand thereof-   or the isolated nucleic acid molecule of embodiment 4 or the vector    of embodiment 7 is used to screen and isolate nucleic acid sequences    derived from the plant.

Embodiment 16: A transgenic plant, plant cell or plant materialcomprising a cell according to any one of embodiment 8 or producedaccording to a method according to any one of embodiments 13 or 14 orprogeny thereof.

Embodiment 17: The transgenic plant, plant cell or plant materialaccording to embodiment 16 transgenically expressing the nucleotide acidsequence of any one of embodiments 5 or 6.

Embodiment 18: A method for identifying an effector for apomixis in aplant, wherein the transgenic plant, plant cell or plant materialaccording to any one of embodiments 16 or 17 is cultivated.

Further preferred embodiments of the present invention are the subjectmatter of the subclaims.

The invention will now be illustrated by way of example.

EXAMPLE 1 Screening and Isolation of Apomixis-Inducing Gene (ApolloGene) 1.a) Plant Material and Seed Screen Analysis

Plants were grown from seedlings onwards in a phytotron under controlledenvironmental conditions. The flow cytometric seed screen was used toanalyse reproductive variability in 18 Boechera accessions (Table IV).

TABLE IV Boechera accessions used in Microarrays and RT-PCR analyses.Apomeiosis Accession frequency Collection locality B08-1 1 Birch Creek,Montana B08-11 1 Sliderock, Ranch Creek, Granite, Montana B08-33 1 MuleRanch, Montana B08-111 1 Morgan Switch Back, Idaho B08-81 1 Vipond Park,Beaverhead, Montana B08-168 1 Vipond Park, Beaverhead, Montana B08-43 1Mule Ranch, Montana B08-66 1 Highwood Mtns, Montana B08-104 1 Lost TrailMeadow B08-215 1 Blue Lakes road, California B08-369 0 Twin Saddle,Idaho B08-376 0 Sagebrush Meadow, Montana B08-380 0 Buffalo Pass,Colorado B08-355 0 Gold Creek, Colorado B08-329 0 Big Hole Pass, MontanaB08-385 0 Parker Meadow, Idaho B08-344 0 Bandy Ranch, Montana B08-390 0Panther Creek

Single seeds were ground individually with three 2.3 mm stainless steelbeads in each well of 96-well plate (PP-Master-block 128.0/85 MM, 1.0 ml96 well plate by Greiner bio-one, on the world wide web at “gbo.com”)containing 50 μl extraction-nuclei isolation buffer (see below) using aGeno-Grinder 2000 (SPEX Certi-Prep) at rate of 150 strokes/minute for 90seconds.

A two-step procedure consisting of an isolation and staining buffer wasused: (a) isolation buffer I—0.1M Citric acid monohydrate and 0.5% v/vTween 20 dissolved in H₂O and adjusted to pH 2.5); and (b) stainingbuffer II—0.4M Na₂HPO₄.12H₂O dissolved in H₂O plus 4 μg/ml4′,6-Diamidinophenyl-indole (DAPI) and adjusted to pH 8.5. 50 μl ofisolation buffer I was added to each seed per well in a 96-well platebefore grinding, and a further 160 μl buffer I was added after grindingto recover enough volume through filtration (using Partec 30 μmmesh-width nylon filters). 100 μl of staining buffer II was then addedto 50 μl of the resultant suspension (isolated nuclei), and incubated onice for 10 minutes before flow cytometric analysis. To avoid sampledegradation over the 2-hour period required for the analysis of 96samples, the sample plate was sealed with aluminum sealing tape.

All sample plates were analysed on a 4° C. cooled Robby-Wellauto-sampler hooked up to a Partec PAII flow Cytometer (Partec GmbH,Münster, Germany). Two single seeds from SAD 12, a known sexualself-fertile Boechera were always included as an external reference atwell positions 1 and 96 in order to normalize other peaks and correctpeak shifts over the analysis period. SAD 12 seeds were composedexclusively of 2C embryo to 3C endosperm ratio, which reflected anembryo composition of C (C denotes monoploid DNA content) maternal (Cm)genomes+C paternal (Cp)=2 C genomes, and an endosperm composition of 2Cm+Cp=3 C.

Based upon the present high-throughput flow-cytometric seed screen data,all apomictic accessions were shown to be characterized by 100%apomictic seed production.

1.b) Ovule Micro-Dissection

Ovules at megasporogenesis between stages 2-II to 2-IV were selectedwhere megaspore mother cell is differentiated, inner and outerintegument initiated in order to examine changes in gene expressionassociated with meiosis and apomeiosis. The gynoecia of sexual andapomictic Boechera were dissected out from non-pollinated flowers at thestage of megasporogenesis in 0.55 M sterile mannitol solution, at astandardized time (between 8 and 9 a.m.) over multiple days.Microdissections were done in a sterile laminar air flow cabinet using astereoscopic Microscope (1000 Stemi, Carl Zeiss, Jena, Germany) under 2×magnification. The gynoecium was held with forceps while a sterilescalpel was used to cut longitudinally such that the halves of thesilique along with the ovules were immediately exposed to the mannitol.Individual live ovules were subsequently collected under an invertedMicroscope (Axiovert 200M, Carl Zeiss) in sterile conditions, usingsterile glass needles (self-made using a Narishige PC-10 puller, andbent to an angle of about 100°) to isolate the ovules from placentaltissue. Using a glass capillary (with an opening of 150 μm interiordiameter) interfaced to an Eppendorf Cell Tram Vario, the ovules werecollected in sterile Eppendorf tubes containing 100 μl of RNAstabilizing buffer (RNA later, Sigma). Between 20 and 40 ovules peraccession were collected in this way, frozen directly in liquid nitrogenand stored at −80° C.

1.c) Ovule RNA Isolation

Total RNA extractions were carried out using PicoPure RNA isolation kit(Arcturus Bioscience, CA). RNA integrity and quantity was verified on anAgilent 2100 Bioanalyzer using the RNA Pico chips (Agilent Technologies,Palo Alto, Calif.).

1.d) Microarray 1.d.i) Microarray Design

The 454 (FLX) technology was used to sequence the completetranscriptomes of 3 sexual and 3 apomictic Boechera accessions, as afirst step in the design of high-density Boechera-specific microarraysfor use in comparisons of gene expression and copy number variation. Thegoal of transcriptome sequencing was thus to identify all genes whichcan be expressed during flower development, followed by the spotting ofall identified genes onto an (Agilent) microarray.

This was accomplished by pooling flowers at multiple developmentalstages separately for sexual and apomictic plants, followed by a cDNAnormalization procedure in order to balance out transcript levels toincrease the chance that all observable mRNA species are sequenced.Furthermore, a 3′-UTR (untranslated region) anchored 454 procedure wasemployed such that mRNA sequences were biased towards their 3′-UTRs,regions which demonstrate relatively high (but not random) levels ofvariability, to enable the identification of allelic variation.

The 454 sequences were assembled using the CLC Genomics workbench usingstandard assembly parameters for long-read high-throughput sequences,after trimming of all reads using internal sequence quality scores. Indoing so, 36 289 contig sequences and 154 468 non-assembled singletonsequences were obtained. This data was provided to ImaGenes (GmbH,Germany) for microarray development using their Pre-selection strategy(PSS) service.

The PSS service worked as follows: 14 different oligonucleotides (each60 bp in length) per contig and 8 oligonucleotides per singleton,including the “anti-sense” sequence of each oligo, werebioinformatically designed and spotted onto two 1 million-spot testarrays. These test-arrays were probed using (1) a “complex cRNA mixture”(obtained by pooling tissues and harvesting all RNA from them), and (2)genomic DNA extracted from leaf tissue pooled from a sexual and anapomictic individual. Based upon the separate hybridization results fromthe cRNA and genomic DNA samples, and after all quality tests, a final2×105 000 spot array was designed. This array should contain multipleoligonucleotides (i.e. technical replicates) of every gene expressedduring Boechera flower development.

1.d.ii) Hybridization

cRNA was prepared and labelled using the Quick-Amp One-Color LabelingKit (Agilent Technologies, CA) and hybridized to the Agilent customBoechera arrays (8 and 10 biological replicates were hybridized forsexual and apomictic genotypes respectively).

1.d.iii) Statistical Analysis

Analyses were performed using GeneSpring GX Software (version 10) andcandidate probes significantly differentially expressed (p≤0.05) betweenapomictic and sexual plants were selected based on the followingparameters: (a) percentile shift 75 normalization, median as baseline,reproductive mode (apomictic or sexual) as interpretation (1st level),T-test unpaired as statistical analysis and Bonferroni FWER multipletest corrections. Using the highest level of significance cutoff led tothe identification of 4 different spots on the microarray (p<0.01 forthe first three and p<0.05 for the fourth). Importantly, when theoligonucleotide sequences of these 4 spots were BLASTed to a 454 cDNAsequence database, all 4 blasted to the same Boechera transcript. Thus,not only has the present experiment been corrected for biological noise,furthermore a single differentially-expressed transcript between themicrodissected ovules of all sexual and apomictic genotypes, with 4technical replicates for the specific gene on the microarray wasdetected. This gene is expressed to a similar fashion when comparingboth diploid and triploid apomictic ovules to those of sexuals, andhence its expression behavior is apparently not influenced by ploidy.Finally, a search for homologues to this Boechera transcriptdemonstrated that it is involved with the cell cycle in other species,thus supporting evidence regarding deregulation of the sexual pathway asa means to produce apomixis.

EXAMPLE 2 Characterisation of Apomixis-Inducing Gene 2.a) Candidate GeneCharacterization 2.a.i) Genome Level 2.a.i.1) Cloning

The full-length transcript from all 18 accessions was cloned andsequenced (TOPO-TA Cloning kit, Invitrogen) using proofreadingpolymerase (Accuprime). The transcript is highly polymorphic, and ischaracterized by comparable levels of single nucleotide polymorphismsbetween sexual and apomicts. Nevertheless, a single “apomixispolymorphism” is found in all 10 apomictic accessions, but not in anysexual accession. SEQ ID No. 46 to 54 show the genomic and the codingsequence of three sexual alleles, namely S011a, S355a and S390a. SEQ IDNo. 37 to 45 show the genomic and the coding sequence of three apomicticalleles, namely A011a, A043a and A081a. Considering that the geographiccollection points of all accessions range from California to theAmerican mid-west (i.e. 1000's of kilometers), the sharing of thispolymorphism in all apomicts is highly significant. Finally, the SNPpolymorphism spectrum surrounding the “apomixis polymorphism” reflectsthat found in all other alleles in both sexual and apomictic accessions.Hence the “apomixis polymorphism” appears to have undergonerecombination during the evolution of Boechera, but which is nonethelessshared by all apomicts, regardless of different genetic, ploidy orgeographic backgrounds.

2.a.i.2) BAC

Pooled DNA of all tissues accessions was used as a template forhybridization probes generation. Two probes of different size (1.6 and2.3 kb) were prepared by PCR amplification using two pairs of specificprimers of the candidate gene genomic sequence. Both probes were labeledand used for hybridization on a apomictic Boechera BAC library. Therewere 8 positive hybridizations. The respective isolated BACs (PureLinkPlasmid DNA Purification kit) were named 1, 2a, 2b, 3, 4, 5, 6 and 7.Selected BACs were retested using specific primers for the candidategene. All BACs were confirmed except the BAC-3. The other seven BACswere fingerprinted by restriction enzyme digestion. BAC-1 and BAC-2aseemed to be redundant with the other BACs. The BACs: 2b, 4, 5, 6 and 7were sequenced.

BAC sequences could be assembled together for the pairs 2b_4 and 5_7,whereas BAC-6 remained alone.

BAC sequences were characterized by comparison with other plantsequences.

2.a.ii) Transcriptome Level

RACE experiments (SMARTer RACE cDNA Amplification Kit) were performed.

The results revealed that mRNA corresponding to apomictic accessions hasa truncated 5′ extreme upstream the “apomixis polymorphism” whereassexual accessions have ˜200 bp of additional length.

Once 5′ and 3′ mRNA extremes were known, further PCRs over all tissuescDNA were performed for complete splicing profile characterization.

2.b) Validation 2.b.i) QRT-PCR

An allele-specific qRT-PCR analysis of the candidate gene on themicrodissected live ovules (megaspore mother cell stage) from 6 sexualand 10 diploid apomictic Boechera accessions (3 technical replicates peraccession) was completed. Using two different forward PCR primers whichspanned the apomixis-specific polymorphism which was identified from thegene sequences, it was possible to measure transcript abundance for boththe sexual and apomictic alleles separately.

cDNA was prepared using RevertAid H Minus reverse transcriptase.

For the real-time PCR reactions the SYBR® Green PCR Master Mix (AppliedBiosystems, Foster City, Calif.) was used. QRT-PCR amplifications werecarried out in a 7900HT Fast RT-PCR System machine (Applied Biosystems)with the following temperature profile for SYBRgreen assays: initialdenaturation at 90° C. for 10 min, followed by 40 cycles of 95° C. for15 sec. and 60° C. for 1 min. For checking amplicon quality, a meltingcurve gradient was obtained from the product at the end of theamplification. The Ct, defined as the PCR cycle at which a statisticallysignificant increase of reporter fluorescence is first detected, wasused as a measure for the starting copy numbers of the target gene. Themean expression level and standard deviation for each set of threetechnical replicates for each cDNA was calculated. Relative quantitationand normalization of the amplified targets were performed by thecomparative ΔΔCt method using a calibrator sample in reference to theexpression levels of the house-keeping gene UBQ10.

The results are conclusive: the apomictic allele is exclusivelyexpressed in the microdissected ovules of all apomictic accessions,while the sexual allele is never expressed in any, which means sexual orapomictic, ovule. Both alleles are expressed in other tissues, namelysomatic tissue. Hence, it appears very reasonable to assume that thesexual allele is inactive/silenced during normal sexual ovuledevelopment, while the expression of the apomictic allele is correlatedwith apomeiotic ovule development.

EXAMPLE 3 Construction of Transformation Vectors and Transformation ofArabidopsis thaliana with Apomixis-Inducing Gene Plant Transformation

Transformations of Arabidopsis thaliana (sex) (hybrids F1) and Boechera(sex) with the gene of the present invention are able to show a changeof their reproductive mode into apomictic seed production. For this, thecomplete genomic allele (including complete promoter) has been cloned inpNOS-ABM.

In addition, different constructs are used to characterize the role ofthe present regulatory elements, in particular the promoter of thepresent invention, in its expression. For this, both apo and sexpromoters have been exactly connected to the ATG in front of gus inpGUS-ABM.

Complete BAC-4 is as well used for transformations.

1. An isolated nucleic acid molecule for use in inducing apomixis in aplant comprising a polynucleotide, which is selected from the groupconsisting of a) the polynucleotide defined in any one of SEQ ID No. 22to 62, or a fully complementary strand thereof, b) a polynucleotideencoding a polypeptide with the amino acid sequence defined in any oneof SEQ ID No. 1 to 21 or a fully complementary strand thereof, and c) apolynucleotide variant having a degree of sequence identity of more than70% to the nucleic acid sequence defined in a) or b), or a fullycomplementary strand thereof.
 2. The isolated nucleic acid molecule ofclaim 1, which comprises a polynucleotide coding for a protein withexonuclease activity, which polynucleotide is selected from the groupconsisting of a1) the polynucleotide defined in any one of SEQ ID No. 22to 54, or a fully complementary strand thereof, b1) a polynucleotideencoding a polypeptide with the amino acid sequence defined in any oneof SEQ ID No. 1 to 21 or a fully complementary strand thereof, and c1) apolynucleotide variant having a degree of sequence identity of more than70% to the nucleic acid sequence defined in a1) or b1), or a fullycomplementary strand thereof.
 3. The isolated nucleic acid molecule ofclaim 2, wherein the polynucleotide comprises a nucleic acid sequenceselected from the group consisting of a2) the polynucleotide defined inany one of SEQ ID No. 22, 23, 27, 28, 32, 33 or a fully complementarystrand thereof, b2) a polynucleotide encoding a polypeptide with theamino acid sequence defined in any one of SEQ ID No. 4, 5, 6 or a fullycomplementary strand thereof, and c2) a polynucleotide variant having adegree of sequence identity of more than 70% to the nucleic acidsequence defined in a2) or b2), or a fully complementary strand thereof.4. The isolated nucleic acid molecule of claim 1, which comprises apolynucleotide which polynucleotide is able to act as a regulatoryelement and is selected from the group consisting of a3) thepolynucleotide defined in any one of SEQ ID No. 55 to 62 or 65 or afully complementary strand thereof and b3) a polynucleotide varianthaving a degree of sequence identity of more than 70% to the nucleicacid sequence defined in a3), or a fully complementary strand thereof.5. A vector comprising the nucleic acid molecule of any one of claims 1to
 4. 6. The vector of claim 5, wherein the nucleic acid molecule of anyone of claims 1 to 3 is operably linked to at least one regulatoryelement.
 7. The vector of claim 5 or 6, wherein the nucleic acidmolecule of any one of claim 1 or 4 is operably linked to at least oneprotein coding nucleotide sequence.
 8. A host cell containing the vectorof claims 5 to
 7. 9. A protein encoded by a nucleotide acid sequenceaccording to any one of claims 1 to
 3. 10. A transgenic plant, plantcell or plant material comprising at least one transgenic nucleic acidmolecule of any one of claims 1 to 4 or the vector of any one of claims5 to
 7. 11. A cell culture, preferably a plant cell culture comprising acell according to claim
 8. 12. A method for inducing apomixis in aplant, wherein the expression of a nucleotide sequence encoding aprotein capable of inducing apomixis in a plant according to any one ofclaims 1 to 3 is induced in the ovule of said plant.
 13. The method forinducing apomixis in a plant according to claim 12, wherein theexpression is induced by transforming a plant cell with the isolatednucleic acid molecule of any one of claims 1 to 4 or the vectoraccording to any one of claims 5 to 7 and regenerating the transformedplant cell into a transformed plant that contains the at least onenucleic acid sequence according to claims 1 to 4 so as to induceapomixis in the plant.
 14. A method for the production of an apomicticplant, wherein a plant cell is transformed with a nucleic acid moleculecapable of inducing the expression of nucleotide sequence encoding aprotein capable of inducing apomixis in a plant according to any one ofclaims 1 to 4 and regenerating the transformed plant cell into atransformed plant that contains the nucleic acid molecule so as toinduce apomixis in the plant.
 15. The method for the production of anapomictic plant by transforming according to claim 14, wherein the plantcell is transformed with the isolated nucleic acid molecule of any oneof claims 1 to 4 or the vector of claims 5 to 7 and the transformedplant cell is regenerated into a transformed plant that contains the atleast one nucleic acid sequence according to claims 1 to 4 so as toinduce apomixis in the plant.
 16. A method for isolating an apomixisinducing nucleic acid molecule from a plant, wherein the isolatednucleic acid molecule of any one of claims 1 to 4 is used to screen andisolate nucleic acid sequences derived from the plant.
 17. A transgenicplant, plant cell or plant material comprising a cell according to anyone of claim 8, 10 or 11 or produced according to a method according toany one of claim 14 or 15 or progeny thereof.
 18. The transgenic plant,plant cell or plant material according to claim 17 transgenicallyexpressing the nucleotide acid sequence of any one of claims 1 to
 4. 19.A method for identifying an effector for apomixis in a plant, whereinthe transgenic plant, plant cell or plant material according to any oneof claim 17 or 18 is cultivated.